I would need to see more pictures of the entire tree and of the larger branches, especially showing the transition from unhealthy to healthy tissue.  The initial damage could be on theses bigger branches or trunk, and the ends of branches die back because their food & water supply are shut off.  Diagnosis focuses on the initial site of damage which could be cold damage, insects, disease, etc.

My major concern is this canker on the base of the tree.  See attached picture.  I would guess that this extends into the tree, having a major disruption on water, mineral, and sugar transport.  At this time it is difficult to know why the canker started...mechanical injury is a common cause, also could be winter injury.   It weakens the tree, allowing it to be susceptible to various fungal pathogens.  

Really not much that can be done on such a big zone on a young tree since it is on the trunk.  If it was a side branch, pruning would be an option.

Do a thorough job of removing roots and branch remnants.   That should be sufficient.  

We really don't know what caused the initial injury. If the soil is heavy texture and tends to remain soggy for more than a day following a heavy rain you could consider shoveling in some lighter soil and mixing well before planting.   If it is in danger of being hit by mowers, etc, you can put a wire mesh screen around the base.   

Here's some additional tips.

https://williamshane.weebly.com/uploads/2/7/0/7/27077603/getting_fruit_trees_off_to_a_good_start_shane_feb_2016.pdf

You are welcome